Sliding Windows Analysis

Blueback Populations, Size 50kb step 10kb

AlR_HdR_plot <- ggplot(data = AlR_HdR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = AlR_HdR_axis_set$chr, 
                     breaks = AlR_HdR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(AlR_HdR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Altamaha R. vs Hudson R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
AlR_HdR_plot

AlR_PtR_plot <- ggplot(data = AlR_PtR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = AlR_PtR_axis_set$chr, 
                     breaks = AlR_PtR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(AlR_PtR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Altamaha R. vs Petitcodiac R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
AlR_PtR_plot

LkH_AlR_plot <- ggplot(data = LkH_AlR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = LkH_AlR_axis_set$chr, 
                     breaks = LkH_AlR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(LkH_AlR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "L. Hartwell vs Altamaha R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
LkH_AlR_plot

LkH_HdR_plot <- ggplot(data = LkH_HdR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = LkH_HdR_axis_set$chr, 
                     breaks = LkH_HdR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(LkH_HdR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "L. Hartwell vs Hudson R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
LkH_HdR_plot

LkH_LkY_plot <- ggplot(data = LkH_LkY, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = LkH_LkY_axis_set$chr, 
                     breaks = LkH_LkY_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(LkH_LkY_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "L. Hartwell vs L. Yonah Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
LkH_LkY_plot

LkH_PtR_plot <- ggplot(data = LkH_PtR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = LkH_PtR_axis_set$chr, 
                     breaks = LkH_PtR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(LkH_PtR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "L. Hartwell vs Petitcodiac R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
LkH_PtR_plot

LkY_AlR_plot <- ggplot(data = LkY_AlR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = LkY_AlR_axis_set$chr, 
                     breaks = LkY_AlR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(LkY_AlR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "L. Yonah vs Altamaha R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
LkY_AlR_plot

LkY_HdR_plot <- ggplot(data = LkY_HdR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = LkY_HdR_axis_set$chr, 
                     breaks = LkY_HdR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(LkY_HdR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "L. Yonah vs Hudson R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
LkY_HdR_plot

LkY_PtR_plot <- ggplot(data = LkY_PtR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = LkY_PtR_axis_set$chr, 
                     breaks = LkY_PtR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(LkY_PtR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "L. Yonah vs Petitcodiac R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
LkY_PtR_plot

PtR_HdR_plot <- ggplot(data = PtR_HdR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = PtR_HdR_axis_set$chr, 
                     breaks = PtR_HdR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(PtR_HdR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Petitcodiac R. vs Hudson R. Blueback", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
PtR_HdR_plot

### Using ggsave to save the manhattan plots, or as I will now refer to it: ###
# Saving Private Plots (Ryan lol) ##
ggsave("figures/sliding-windows-fst/MIDA-x-NATLA-sz50-chrom19-spike.png", 
       plot = mxn50_chr19_spike_plot, 
       width = 10, 
       height = 4)